X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=d472ef81f7f6b4a2c44d68ea07c2e84aefda9a59;hb=62d2ca926e73609acc4c2a50676f2010c6e3e343;hp=68184e9d06bc2b1dfba3d66adc05db9d83992e79;hpb=e2e2b85d7a8e3d7ed6926ef1bf55eb2328e744d1;p=jalview.git

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 68184e9..d472ef8 100644
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -29,6 +29,7 @@ import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.RnaViewerModel;
 import jalview.datamodel.SequenceGroup;
@@ -77,7 +78,6 @@ import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.FeatureColour;
-import jalview.schemes.ResidueColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.UserColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -87,6 +87,7 @@ import jalview.util.Platform;
 import jalview.util.StringUtils;
 import jalview.util.jarInputStreamProvider;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.ViewportRanges;
 import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
 import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
 import jalview.ws.jws2.Jws2Discoverer;
@@ -179,13 +180,13 @@ public class Jalview2XML
    * Map of reconstructed AlignFrame objects that appear to have come from
    * SplitFrame objects (have a dna/protein complement view).
    */
-  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<Viewport, AlignFrame>();
+  private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
 
   /*
    * Map from displayed rna structure models to their saved session state jar
    * entry names
    */
-  private Map<RnaModel, String> rnaSessions = new HashMap<RnaModel, String>();
+  private Map<RnaModel, String> rnaSessions = new HashMap<>();
 
   /**
    * create/return unique hash string for sq
@@ -246,19 +247,19 @@ public class Jalview2XML
   {
     if (seqsToIds == null)
     {
-      seqsToIds = new IdentityHashMap<SequenceI, String>();
+      seqsToIds = new IdentityHashMap<>();
     }
     if (seqRefIds == null)
     {
-      seqRefIds = new HashMap<String, SequenceI>();
+      seqRefIds = new HashMap<>();
     }
     if (incompleteSeqs == null)
     {
-      incompleteSeqs = new HashMap<String, SequenceI>();
+      incompleteSeqs = new HashMap<>();
     }
     if (frefedSequence == null)
     {
-      frefedSequence = new ArrayList<SeqFref>();
+      frefedSequence = new ArrayList<>();
     }
   }
 
@@ -457,9 +458,9 @@ public class Jalview2XML
    * This maintains a map of viewports, the key being the seqSetId. Important to
    * set historyItem and redoList for multiple views
    */
-  Map<String, AlignViewport> viewportsAdded = new HashMap<String, AlignViewport>();
+  Map<String, AlignViewport> viewportsAdded = new HashMap<>();
 
-  Map<String, AlignmentAnnotation> annotationIds = new HashMap<String, AlignmentAnnotation>();
+  Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
 
   String uniqueSetSuffix = "";
 
@@ -535,7 +536,7 @@ public class Jalview2XML
    */
   private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
   {
-    Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+    Hashtable<String, AlignFrame> dsses = new Hashtable<>();
 
     /*
      * ensure cached data is clear before starting
@@ -550,8 +551,8 @@ public class Jalview2XML
       // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
       // //////////////////////////////////////////////////
 
-      List<String> shortNames = new ArrayList<String>();
-      List<String> viewIds = new ArrayList<String>();
+      List<String> shortNames = new ArrayList<>();
+      List<String> viewIds = new ArrayList<>();
 
       // REVERSE ORDER
       for (int i = frames.size() - 1; i > -1; i--)
@@ -661,7 +662,7 @@ public class Jalview2XML
     {
       FileOutputStream fos = new FileOutputStream(jarFile);
       JarOutputStream jout = new JarOutputStream(fos);
-      List<AlignFrame> frames = new ArrayList<AlignFrame>();
+      List<AlignFrame> frames = new ArrayList<>();
 
       // resolve splitframes
       if (af.getViewport().getCodingComplement() != null)
@@ -747,14 +748,15 @@ public class Jalview2XML
   {
     if (viewIds == null)
     {
-      viewIds = new ArrayList<String>();
+      viewIds = new ArrayList<>();
     }
 
     initSeqRefs();
 
-    List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
+    List<UserColourScheme> userColours = new ArrayList<>();
 
     AlignViewport av = ap.av;
+    ViewportRanges vpRanges = av.getRanges();
 
     JalviewModel object = new JalviewModel();
     object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
@@ -805,9 +807,9 @@ public class Jalview2XML
     }
 
     JSeq jseq;
-    Set<String> calcIdSet = new HashSet<String>();
+    Set<String> calcIdSet = new HashSet<>();
     // record the set of vamsas sequence XML POJO we create.
-    HashMap<String, Sequence> vamsasSetIds = new HashMap<String, Sequence>();
+    HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
     // SAVE SEQUENCES
     for (final SequenceI jds : rjal.getSequences())
     {
@@ -984,7 +986,7 @@ public class Jalview2XML
             pdb.setFile(matchedFile); // entry.getFile());
             if (pdbfiles == null)
             {
-              pdbfiles = new ArrayList<String>();
+              pdbfiles = new ArrayList<>();
             }
 
             if (!pdbfiles.contains(pdbId))
@@ -1105,7 +1107,7 @@ public class Jalview2XML
               Tree tree = new Tree();
               tree.setTitle(tp.getTitle());
               tree.setCurrentTree((av.currentTree == tp.getTree()));
-              tree.setNewick(tp.getTree().toString());
+              tree.setNewick(tp.getTree().print());
               tree.setThreshold(tp.treeCanvas.threshold);
 
               tree.setFitToWindow(tp.fitToWindow.getState());
@@ -1133,7 +1135,7 @@ public class Jalview2XML
     /**
      * store forward refs from an annotationRow to any groups
      */
-    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<SequenceGroup, String>();
+    IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
     if (storeDS)
     {
       for (SequenceI sq : jal.getSequences())
@@ -1270,8 +1272,8 @@ public class Jalview2XML
       view.setWidth(size.width);
       view.setHeight(size.height);
 
-      view.setStartRes(av.startRes);
-      view.setStartSeq(av.startSeq);
+      view.setStartRes(vpRanges.getStartRes());
+      view.setStartSeq(vpRanges.getStartSeq());
 
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
@@ -1347,7 +1349,7 @@ public class Jalview2XML
                 .getFeatureRenderer().getRenderOrder()
                 .toArray(new String[0]);
 
-        Vector<String> settingsAdded = new Vector<String>();
+        Vector<String> settingsAdded = new Vector<>();
         if (renderOrder != null)
         {
           for (String featureType : renderOrder)
@@ -1390,7 +1392,7 @@ public class Jalview2XML
         // is groups actually supposed to be a map here ?
         Iterator<String> en = ap.getSeqPanel().seqCanvas
                 .getFeatureRenderer().getFeatureGroups().iterator();
-        Vector<String> groupsAdded = new Vector<String>();
+        Vector<String> groupsAdded = new Vector<>();
         while (en.hasNext())
         {
           String grp = en.next();
@@ -1411,18 +1413,18 @@ public class Jalview2XML
 
       if (av.hasHiddenColumns())
       {
-        if (av.getColumnSelection() == null
-                || av.getColumnSelection().getHiddenColumns() == null)
+        jalview.datamodel.HiddenColumns hidden = av.getAlignment()
+                .getHiddenColumns();
+        if (hidden == null)
         {
           warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
         }
         else
         {
-          for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
-                  .size(); c++)
+          ArrayList<int[]> hiddenRegions = hidden
+                  .getHiddenColumnsCopy();
+          for (int[] region : hiddenRegions)
           {
-            int[] region = av.getColumnSelection().getHiddenColumns()
-                    .get(c);
             HiddenColumns hc = new HiddenColumns();
             hc.setStart(region[0]);
             hc.setEnd(region[1]);
@@ -1711,6 +1713,15 @@ public class Jalview2XML
     return matchedFile;
   }
 
+  /**
+   * Populates the AnnotationColours xml for save. This captures the settings of
+   * the options in the 'Colour by Annotation' dialog.
+   * 
+   * @param acg
+   * @param userColours
+   * @param jms
+   * @return
+   */
   private AnnotationColours constructAnnotationColours(
           AnnotationColourGradient acg, List<UserColourScheme> userColours,
           JalviewModelSequence jms)
@@ -1718,8 +1729,9 @@ public class Jalview2XML
     AnnotationColours ac = new AnnotationColours();
     ac.setAboveThreshold(acg.getAboveThreshold());
     ac.setThreshold(acg.getAnnotationThreshold());
-    ac.setAnnotation(acg.getAnnotation());
-    if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+    // 2.10.2 save annotationId (unique) not annotation label
+    ac.setAnnotation(acg.getAnnotation().annotationId);
+    if (acg.getBaseColour() instanceof UserColourScheme)
     {
       ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
               userColours, jms));
@@ -2277,7 +2289,7 @@ public class Jalview2XML
     try
     {
       // create list to store references for any new Jmol viewers created
-      newStructureViewers = new Vector<JalviewStructureDisplayI>();
+      newStructureViewers = new Vector<>();
       // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
       // Workaround is to make sure caller implements the JarInputStreamProvider
       // interface
@@ -2370,8 +2382,8 @@ public class Jalview2XML
       initSeqRefs();
     }
     AlignFrame af = null, _af = null;
-    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<AlignmentI, AlignmentI>();
-    Map<String, AlignFrame> gatherToThisFrame = new HashMap<String, AlignFrame>();
+    IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+    Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
     final String file = jprovider.getFilename();
     try
     {
@@ -2512,9 +2524,9 @@ public class Jalview2XML
    */
   protected void restoreSplitFrames()
   {
-    List<SplitFrame> gatherTo = new ArrayList<SplitFrame>();
-    List<AlignFrame> addedToSplitFrames = new ArrayList<AlignFrame>();
-    Map<String, AlignFrame> dna = new HashMap<String, AlignFrame>();
+    List<SplitFrame> gatherTo = new ArrayList<>();
+    List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+    Map<String, AlignFrame> dna = new HashMap<>();
 
     /*
      * Identify the DNA alignments
@@ -2639,10 +2651,12 @@ public class Jalview2XML
           @Override
           public void run()
           {
-            JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                    finalErrorMessage, "Error "
-                            + (saving ? "saving" : "loading")
-                            + " Jalview file", JvOptionPane.WARNING_MESSAGE);
+            JvOptionPane
+                    .showInternalMessageDialog(Desktop.desktop,
+                            finalErrorMessage, "Error "
+                                    + (saving ? "saving" : "loading")
+                                    + " Jalview file",
+                            JvOptionPane.WARNING_MESSAGE);
           }
         });
       }
@@ -2654,7 +2668,7 @@ public class Jalview2XML
     errorMessage = null;
   }
 
-  Map<String, String> alreadyLoadedPDB = new HashMap<String, String>();
+  Map<String, String> alreadyLoadedPDB = new HashMap<>();
 
   /**
    * when set, local views will be updated from view stored in JalviewXML
@@ -2825,7 +2839,7 @@ public class Jalview2XML
 
     List<SequenceI> hiddenSeqs = null;
 
-    List<SequenceI> tmpseqs = new ArrayList<SequenceI>();
+    List<SequenceI> tmpseqs = new ArrayList<>();
 
     boolean multipleView = false;
     SequenceI referenceseqForView = null;
@@ -2893,7 +2907,7 @@ public class Jalview2XML
       {
         if (hiddenSeqs == null)
         {
-          hiddenSeqs = new ArrayList<SequenceI>();
+          hiddenSeqs = new ArrayList<>();
         }
 
         hiddenSeqs.add(tmpSeq);
@@ -3101,12 +3115,12 @@ public class Jalview2XML
 
     // ////////////////////////////////
     // LOAD ANNOTATIONS
-    List<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+    List<JvAnnotRow> autoAlan = new ArrayList<>();
 
     /*
      * store any annotations which forward reference a group's ID
      */
-    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, List<AlignmentAnnotation>>();
+    Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
 
     if (vamsasSet.getAnnotationCount() > 0)
     {
@@ -3261,7 +3275,7 @@ public class Jalview2XML
                   .get(an[i].getGroupRef());
           if (aal == null)
           {
-            aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+            aal = new ArrayList<>();
             groupAnnotRefs.put(an[i].getGroupRef(), aal);
           }
           aal.add(jaa);
@@ -3351,7 +3365,7 @@ public class Jalview2XML
         }
         int pidThreshold = jGroup.getPidThreshold();
 
-        Vector<SequenceI> seqs = new Vector<SequenceI>();
+        Vector<SequenceI> seqs = new Vector<>();
 
         for (int s = 0; s < jGroup.getSeqCount(); s++)
         {
@@ -3744,7 +3758,7 @@ public class Jalview2XML
      * Run through all PDB ids on the alignment, and collect mappings between
      * distinct view ids and all sequences referring to that view.
      */
-    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<String, StructureViewerModel>();
+    Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
 
     for (int i = 0; i < jseqs.length; i++)
     {
@@ -3942,8 +3956,8 @@ public class Jalview2XML
 
     Set<Entry<File, StructureData>> fileData = data.getFileData()
             .entrySet();
-    List<PDBEntry> pdbs = new ArrayList<PDBEntry>();
-    List<SequenceI[]> allseqs = new ArrayList<SequenceI[]>();
+    List<PDBEntry> pdbs = new ArrayList<>();
+    List<SequenceI[]> allseqs = new ArrayList<>();
     for (Entry<File, StructureData> pdb : fileData)
     {
       String filePath = pdb.getValue().getFilePath();
@@ -3999,9 +4013,9 @@ public class Jalview2XML
               getViewerJarEntryName(svattrib.getViewId()));
     }
 
-    List<String> pdbfilenames = new ArrayList<String>();
-    List<SequenceI[]> seqmaps = new ArrayList<SequenceI[]>();
-    List<String> pdbids = new ArrayList<String>();
+    List<String> pdbfilenames = new ArrayList<>();
+    List<SequenceI[]> seqmaps = new ArrayList<>();
+    List<String> pdbids = new ArrayList<>();
     StringBuilder newFileLoc = new StringBuilder(64);
     int cp = 0, ncp, ecp;
     Map<File, StructureData> oldFiles = svattrib.getFileData();
@@ -4409,13 +4423,6 @@ public class Jalview2XML
 
     }
     // recover view properties and display parameters
-    if (view.getViewName() != null)
-    {
-      af.viewport.viewName = view.getViewName();
-      af.setInitialTabVisible();
-    }
-    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
-            view.getHeight());
 
     af.viewport.setShowAnnotation(view.getShowAnnotation());
     af.viewport.setAbovePIDThreshold(view.getPidSelected());
@@ -4448,8 +4455,16 @@ public class Jalview2XML
     af.viewport.setThresholdTextColour(view.getTextColThreshold());
     af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
             .isShowUnconserved() : false);
-    af.viewport.setStartRes(view.getStartRes());
-    af.viewport.setStartSeq(view.getStartSeq());
+    af.viewport.getRanges().setStartRes(view.getStartRes());
+
+    if (view.getViewName() != null)
+    {
+      af.viewport.viewName = view.getViewName();
+      af.setInitialTabVisible();
+    }
+    af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+            view.getHeight());
+    // startSeq set in af.alignPanel.updateLayout below
     af.alignPanel.updateLayout();
     ColourSchemeI cs = null;
     // apply colourschemes
@@ -4562,8 +4577,8 @@ public class Jalview2XML
       af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
       String[] renderOrder = new String[jms.getFeatureSettings()
               .getSettingCount()];
-      Map<String, FeatureColourI> featureColours = new Hashtable<String, FeatureColourI>();
-      Map<String, Float> featureOrder = new Hashtable<String, Float>();
+      Map<String, FeatureColourI> featureColours = new Hashtable<>();
+      Map<String, Float> featureOrder = new Hashtable<>();
 
       for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
       {
@@ -4622,7 +4637,7 @@ public class Jalview2XML
           fdi.setVisible(setting.getType());
         }
       }
-      Map<String, Boolean> fgtable = new Hashtable<String, Boolean>();
+      Map<String, Boolean> fgtable = new Hashtable<>();
       for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
       {
         Group grp = jms.getFeatureSettings().getGroup(gs);
@@ -4689,12 +4704,21 @@ public class Jalview2XML
     return af;
   }
 
+  /**
+   * Reads saved data to restore Colour by Annotation settings
+   * 
+   * @param viewAnnColour
+   * @param af
+   * @param al
+   * @param jms
+   * @param checkGroupAnnColour
+   * @return
+   */
   private ColourSchemeI constructAnnotationColour(
           AnnotationColours viewAnnColour, AlignFrame af, AlignmentI al,
           JalviewModelSequence jms, boolean checkGroupAnnColour)
   {
     boolean propagateAnnColour = false;
-    ColourSchemeI cs = null;
     AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
     if (checkGroupAnnColour && al.getGroups() != null
             && al.getGroups().size() > 0)
@@ -4702,7 +4726,7 @@ public class Jalview2XML
       // pre 2.8.1 behaviour
       // check to see if we should transfer annotation colours
       propagateAnnColour = true;
-      for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+      for (SequenceGroup sg : al.getGroups())
       {
         if (sg.getColourScheme() instanceof AnnotationColourGradient)
         {
@@ -4710,107 +4734,84 @@ public class Jalview2XML
         }
       }
     }
-    // int find annotation
-    if (annAlignment.getAlignmentAnnotation() != null)
+
+    /*
+     * 2.10.2- : saved annotationId is AlignmentAnnotation.annotationId
+     */
+    String annotationId = viewAnnColour.getAnnotation();
+    AlignmentAnnotation matchedAnnotation = annotationIds.get(annotationId);
+
+    /*
+     * pre 2.10.2: saved annotationId is AlignmentAnnotation.label
+     */
+    if (matchedAnnotation == null && annAlignment.getAlignmentAnnotation() != null)
     {
       for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
       {
-        if (annAlignment.getAlignmentAnnotation()[i].label
-                .equals(viewAnnColour.getAnnotation()))
+        if (annotationId
+                .equals(annAlignment.getAlignmentAnnotation()[i].label))
         {
-          if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
-          {
-            annAlignment.getAlignmentAnnotation()[i]
-                    .setThreshold(new jalview.datamodel.GraphLine(
-                            viewAnnColour.getThreshold(), "Threshold",
-                            java.awt.Color.black)
-
-                    );
-          }
-
-          if (viewAnnColour.getColourScheme().equals(
-                  ResidueColourScheme.NONE))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    new java.awt.Color(viewAnnColour.getMinColour()),
-                    new java.awt.Color(viewAnnColour.getMaxColour()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else if (viewAnnColour.getColourScheme().startsWith("ucs"))
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    getUserColourScheme(jms,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          else
-          {
-            cs = new AnnotationColourGradient(
-                    annAlignment.getAlignmentAnnotation()[i],
-                    ColourSchemeProperty.getColourScheme(al,
-                            viewAnnColour.getColourScheme()),
-                    viewAnnColour.getAboveThreshold());
-          }
-          if (viewAnnColour.hasPerSequence())
-          {
-            ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
-                    .isPerSequence());
-          }
-          if (viewAnnColour.hasPredefinedColours())
-          {
-            ((AnnotationColourGradient) cs)
-                    .setPredefinedColours(viewAnnColour
-                            .isPredefinedColours());
-          }
-          if (propagateAnnColour && al.getGroups() != null)
-          {
-            // Also use these settings for all the groups
-            for (int g = 0; g < al.getGroups().size(); g++)
-            {
-              jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
-
-              if (sg.cs == null)
-              {
-                continue;
-              }
+          matchedAnnotation = annAlignment.getAlignmentAnnotation()[i];
+          break;
+        }
+      }
+    }
+    if (matchedAnnotation == null)
+    {
+      System.err.println("Failed to match annotation colour scheme for "
+              + annotationId);
+      return null;
+    }
+    if (matchedAnnotation.getThreshold() == null)
+    {
+      matchedAnnotation.setThreshold(new GraphLine(viewAnnColour.getThreshold(),
+              "Threshold", Color.black));
+    }
 
-              /*
-               * if (viewAnnColour.getColourScheme().equals(ResidueColourScheme.NONE)) { sg.cs =
-               * new AnnotationColourGradient(
-               * annAlignment.getAlignmentAnnotation()[i], new
-               * java.awt.Color(viewAnnColour. getMinColour()), new
-               * java.awt.Color(viewAnnColour. getMaxColour()),
-               * viewAnnColour.getAboveThreshold()); } else
-               */
-              {
-                sg.setColourScheme(new AnnotationColourGradient(
-                        annAlignment.getAlignmentAnnotation()[i], sg
-                                .getColourScheme(), viewAnnColour
-                                .getAboveThreshold()));
-                if (cs instanceof AnnotationColourGradient)
-                {
-                  if (viewAnnColour.hasPerSequence())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setSeqAssociated(viewAnnColour.isPerSequence());
-                  }
-                  if (viewAnnColour.hasPredefinedColours())
-                  {
-                    ((AnnotationColourGradient) cs)
-                            .setPredefinedColours(viewAnnColour
-                                    .isPredefinedColours());
-                  }
-                }
-              }
+    AnnotationColourGradient cs = null;
+    if (viewAnnColour.getColourScheme().equals("None"))
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation, new Color(
+              viewAnnColour.getMinColour()), new Color(
+              viewAnnColour.getMaxColour()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation, getUserColourScheme(
+              jms, viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
+    else
+    {
+      cs = new AnnotationColourGradient(matchedAnnotation,
+              ColourSchemeProperty.getColourScheme(al,
+                      viewAnnColour.getColourScheme()),
+              viewAnnColour.getAboveThreshold());
+    }
 
-            }
-          }
+    boolean perSequenceOnly = viewAnnColour.isPerSequence();
+    boolean useOriginalColours = viewAnnColour.isPredefinedColours();
+    cs.setSeqAssociated(perSequenceOnly);
+    cs.setPredefinedColours(useOriginalColours);
 
-          break;
+    if (propagateAnnColour && al.getGroups() != null)
+    {
+      // Also use these settings for all the groups
+      for (int g = 0; g < al.getGroups().size(); g++)
+      {
+        SequenceGroup sg = al.getGroups().get(g);
+        if (sg.getGroupColourScheme() == null)
+        {
+          continue;
         }
 
+        AnnotationColourGradient groupScheme = new AnnotationColourGradient(
+                matchedAnnotation, sg.getColourScheme(),
+                viewAnnColour.getAboveThreshold());
+        sg.setColourScheme(groupScheme);
+        groupScheme.setSeqAssociated(perSequenceOnly);
+        groupScheme.setPredefinedColours(useOriginalColours);
       }
     }
     return cs;
@@ -4829,7 +4830,7 @@ public class Jalview2XML
       String[] magicNames = new String[] { "Consensus", "Quality",
           "Conservation" };
       JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
-      Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+      Hashtable<String, JvAnnotRow> visan = new Hashtable<>();
       for (String nm : magicNames)
       {
         visan.put(nm, nullAnnot);
@@ -4841,11 +4842,11 @@ public class Jalview2XML
                         + auan.template.getCalcId()), auan);
       }
       int hSize = al.getAlignmentAnnotation().length;
-      List<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+      List<JvAnnotRow> reorder = new ArrayList<>();
       // work through any autoCalculated annotation already on the view
       // removing it if it should be placed in a different location on the
       // annotation panel.
-      List<String> remains = new ArrayList<String>(visan.keySet());
+      List<String> remains = new ArrayList<>(visan.keySet());
       for (int h = 0; h < hSize; h++)
       {
         jalview.datamodel.AlignmentAnnotation jalan = al
@@ -5173,7 +5174,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
       return null;
     }
     if (datasetIds.containsKey(datasetId))
@@ -5187,7 +5188,7 @@ public class Jalview2XML
   {
     if (datasetIds == null)
     {
-      datasetIds = new Hashtable<String, AlignmentI>();
+      datasetIds = new Hashtable<>();
     }
     datasetIds.put(datasetId, dataset);
   }
@@ -5210,7 +5211,7 @@ public class Jalview2XML
       // make a new datasetId and record it
       if (dataset2Ids == null)
       {
-        dataset2Ids = new IdentityHashMap<AlignmentI, String>();
+        dataset2Ids = new IdentityHashMap<>();
       }
       else
       {
@@ -5489,11 +5490,11 @@ public class Jalview2XML
         // register sequence object so the XML parser can recover it.
         if (seqRefIds == null)
         {
-          seqRefIds = new HashMap<String, SequenceI>();
+          seqRefIds = new HashMap<>();
         }
         if (seqsToIds == null)
         {
-          seqsToIds = new IdentityHashMap<SequenceI, String>();
+          seqsToIds = new IdentityHashMap<>();
         }
         seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
         seqsToIds.put((SequenceI) jvobj, id);